Bioactive stimulation and spatiotemporal evolution of porous scaffolds with time are crucial for bone regeneration rate in bone repair process. Granule-type bioceramic scaffolds have attracted significant interest in biomedical applications in recent years. However, the major limitation of such porous architecture is that the low initial porosity is disadvantageous for enhancing new bone tissue ingrowth. Here we reported that the yolk-shell-structured biphasic bioceramic granules with adjustable shell microstructures were favorable for controllable ion release in vitro, superior to the granules with the conventional homogenous hybrid structures. Also, we illustrated a significant difference in biodegradation of the granules in vivo, and especially the porous-shell granules exhibited appreciable new bone tissue ingrowth with time. The underlying fundamental mechanisms governing the new bone tissue ingrowth behavior of the yolk-shell granule scaffolds were elucidated based on microCT analyses and histological observation. It was underscored that during biodegradation in vivo, the highly bioactive ions in yolk layer were continuously released due to the porous structures of the sparingly dissolvable shell layer, thereby resulting in hollow shell and rapid new bone tissue ingrowth. Hence, these results demonstrate that the slight tailoring in microstructure and component distribution of biphasic composites is beneficial for adjusting the bone regeneration, and may help us to precisely control bone repair efficiency for a variety of clinical conditions.